sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2008-10-15
| Name: | Cyclin-dependent kinase 2 |
|---|---|
| ID: | CDK2_HUMAN |
| AC: | P24941 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 48.520 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.610 | 816.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.56 | 57.44 |
| According to VolSite | |
| HET Code: | I19 |
|---|---|
| Formula: | C24H32FN7O |
| Molecular weight: | 453.556 g/mol |
| DrugBank ID: | DB07936 |
| Buried Surface Area: | 58.29 % |
| Polar Surface area: | 81.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 1.95139 | 27.5529 | 8.79806 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C10 | CD1 | ILE- 10 | 4.12 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 18 | 4.28 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 18 | 3.72 | 0 | Hydrophobic |
| C24 | CB | ALA- 31 | 3.53 | 0 | Hydrophobic |
| N2 | NZ | LYS- 33 | 3.19 | 138.66 | H-Bond (Protein Donor) |
| F1 | CG1 | VAL- 64 | 3.35 | 0 | Hydrophobic |
| C24 | CB | PHE- 80 | 4.12 | 0 | Hydrophobic |
| F1 | CG | PHE- 80 | 3.33 | 0 | Hydrophobic |
| N7 | N | LEU- 83 | 3.1 | 168.71 | H-Bond (Protein Donor) |
| O1 | N | ASP- 86 | 3.06 | 155.02 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 86 | 3.52 | 0 | Ionic (Ligand Cationic) |
| N6 | OD2 | ASP- 86 | 2.98 | 0 | Ionic (Ligand Cationic) |
| N6 | OD2 | ASP- 86 | 2.98 | 142.49 | H-Bond (Ligand Donor) |
| C12 | CB | ASP- 86 | 3.86 | 0 | Hydrophobic |
| C1 | CB | ASN- 132 | 4.21 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 134 | 4.04 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 134 | 3.48 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 134 | 3.34 | 0 | Hydrophobic |
| C5 | CB | ASP- 145 | 3.57 | 0 | Hydrophobic |
